Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold194
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3945165
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1023 characters in sequence are not A, C, G, or T
File 4 of 24
Found at i:528642 original size:11 final size:10
Alignment explanation
Indices: 528622--528650 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
528612 AGCTTTTCTA
528622 TTTTTCTTTT
1 TTTTTCTTTT
528632 TTTTTCTTTT
1 TTTTTCTTTT
528642 TTTTT-TTTT
1 TTTTTCTTTT
528651 CAGAATTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.21
10 15 0.79
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:528645 original size:14 final size:15
Alignment explanation
Indices: 528623--528651 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
528613 GCTTTTCTAT
528623 TTTTCTTTTTTTTTC
1 TTTTCTTTTTTTTTC
528638 TTTT-TTTTTTTTTC
1 TTTTCTTTTTTTTTC
528652 AGAATTAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTCTTTTTTTTTC
Found at i:531119 original size:20 final size:20
Alignment explanation
Indices: 531096--531135 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
531086 TAATTCGAAT
531096 ACACAAAATAAAAAATAAAA
1 ACACAAAATAAAAAATAAAA
531116 ACACAAAATAAAAAATAAAA
1 ACACAAAATAAAAAATAAAA
531136 GTAATTGGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.80, C:0.10, G:0.00, T:0.10
Consensus pattern (20 bp):
ACACAAAATAAAAAATAAAA
Found at i:534629 original size:52 final size:52
Alignment explanation
Indices: 534551--534678 Score: 224
Period size: 52 Copynumber: 2.5 Consensus size: 52
534541 CGAAATATGA
*
534551 AAATTTGCCTGCATGTATCGATACA-TTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAA-AATGTATCGATACATCTGGGC
534603 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
534655 AAA-TTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
534679 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
51 21 0.28
52 48 0.65
53 5 0.07
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
Found at i:534705 original size:13 final size:13
Alignment explanation
Indices: 534687--534711 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
534677 CAAAGATCAG
534687 TGTATCGATACAA
1 TGTATCGATACAA
534700 TGTATCGATACA
1 TGTATCGATACA
534712 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:534789 original size:33 final size:33
Alignment explanation
Indices: 534752--534818 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
534742 AGTAGCTTAA
534752 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
534785 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
534818 A
1 A
534819 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:534792 original size:13 final size:13
Alignment explanation
Indices: 534774--534798 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
534764 CAAAAAAATA
534774 TGTATCGATACAT
1 TGTATCGATACAT
534787 TGTATCGATACA
1 TGTATCGATACA
534799 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:541000 original size:98 final size:98
Alignment explanation
Indices: 540898--541112 Score: 256
Period size: 98 Copynumber: 2.2 Consensus size: 98
540888 TCCTCGGAGT
* * * *
540898 AATGGGGTTGGAGTGT-CTCTAACGATGACAATTTAGGCGAAAATAAGATTTAAATCTTGACAAG
1 AATGGGGTTGGAGTATCCTC-AACGATAACAATTTAAGCAAAAATAAGATTTAAATCTTGACAAG
* * *
540962 TTTAAAAAATGAGGTTAGAGCA-TCCTTTTGAAAG
65 TTAAAAAAATAAGGTTAGAGCATTCC-TTCGAAAG
* * * * *
540996 AATGGGATTAGAGTATCCTCAATGTTAACAATTTAAGCAAAAATAAGATTTAAGTCTTGACAAGT
1 AATGGGGTTGGAGTATCCTCAACGATAACAATTTAAGCAAAAATAAGATTTAAATCTTGACAAGT
* * *
541061 TAAAAAAATAAGGTTGGAGTATTCCTTCGGAAG
66 TAAAAAAATAAGGTTAGAGCATTCCTTCGAAAG
541094 -ATGGGGTTGGAGTATCCTC
1 AATGGGGTTGGAGTATCCTC
541113 GACAAATAAA
Statistics
Matches: 98, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
97 17 0.17
98 75 0.77
99 6 0.06
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.30
Consensus pattern (98 bp):
AATGGGGTTGGAGTATCCTCAACGATAACAATTTAAGCAAAAATAAGATTTAAATCTTGACAAGT
TAAAAAAATAAGGTTAGAGCATTCCTTCGAAAG
Found at i:543847 original size:19 final size:19
Alignment explanation
Indices: 543823--543883 Score: 64
Period size: 19 Copynumber: 3.5 Consensus size: 19
543813 TTCAACAATG
543823 TATCGATACATAAGTGTTT
1 TATCGATACATAAGTGTTT
543842 TATCGATAC--AA-TG---
1 TATCGATACATAAGTGTTT
543855 TATCGATACATAAGT-TTT
1 TATCGATACATAAGTGTTT
543873 GTATCGATACA
1 -TATCGATACA
543884 ATTTAAGCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 14
0.71 0.00 0.29
Matches are distributed among these distances:
13 9 0.26
15 2 0.06
16 3 0.09
17 2 0.06
19 19 0.54
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (19 bp):
TATCGATACATAAGTGTTT
Found at i:543858 original size:32 final size:32
Alignment explanation
Indices: 543817--543885 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
543807 TTGAATTTCA
543817 ACAATGTATCGATACATAAGTGTTT-TATCGAT
1 ACAATGTATCGATACATAAGT-TTTGTATCGAT
543849 ACAATGTATCGATACATAAGTTTTGTATCGAT
1 ACAATGTATCGATACATAAGTTTTGTATCGAT
543881 ACAAT
1 ACAAT
543886 TTAAGCTACT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
31 3 0.08
32 33 0.92
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.36
Consensus pattern (32 bp):
ACAATGTATCGATACATAAGTTTTGTATCGAT
Found at i:543921 original size:13 final size:13
Alignment explanation
Indices: 543903--543929 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
543893 ACTGCCAAAA
543903 ATTGTATCGATAC
1 ATTGTATCGATAC
543916 ATTGTATCGATAC
1 ATTGTATCGATAC
543929 A
1 A
543930 CTGATCTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (13 bp):
ATTGTATCGATAC
Found at i:543979 original size:32 final size:32
Alignment explanation
Indices: 543938--544033 Score: 90
Period size: 32 Copynumber: 3.4 Consensus size: 32
543928 CACTGATCTT
543938 TGTATCGATACATGTAGGAAAATTTGCCCAGA
1 TGTATCGATACATGTAGGAAAATTTGCCCAGA
*
543970 TGTATCGATACAT-TA-TAAAA--T-----G-
1 TGTATCGATACATGTAGGAAAATTTGCCCAGA
*
543992 --TATCGATACATGCAGGAAAATTTGCCCAGA
1 TGTATCGATACATGTAGGAAAATTTGCCCAGA
544022 TGTATCGATACA
1 TGTATCGATACA
544034 CTATTAAATG
Statistics
Matches: 49, Mismatches: 3, Indels: 24
0.64 0.04 0.32
Matches are distributed among these distances:
20 11 0.22
21 1 0.02
22 4 0.08
23 1 0.02
24 1 0.02
28 1 0.02
29 1 0.02
30 4 0.08
31 2 0.04
32 23 0.47
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (32 bp):
TGTATCGATACATGTAGGAAAATTTGCCCAGA
Found at i:543994 original size:52 final size:52
Alignment explanation
Indices: 543938--544059 Score: 217
Period size: 52 Copynumber: 2.3 Consensus size: 52
543928 CACTGATCTT
* *
543938 TGTATCGATACATGTAGGAAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGAAAATTTGCCCAGATGTATCGATACACTATAAAA
*
543990 TGTATCGATACATGCAGGAAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGAAAATTTGCCCAGATGTATCGATACACTATAAAA
544042 TGTATCGATACATGCAGG
1 TGTATCGATACATGCAGG
544060 CAACTTTTCA
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGAAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:545532 original size:13 final size:13
Alignment explanation
Indices: 545514--545539 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
545504 ATATTTTTTG
545514 TGTATCGATACAT
1 TGTATCGATACAT
545527 TGTATCGATACAT
1 TGTATCGATACAT
545540 ATTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:545550 original size:32 final size:33
Alignment explanation
Indices: 545493--545557 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
545483 TACAAGCCAA
545493 TGTATCGATACATATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-TTTTTGTGTATCGATACAT
545527 TGTATCGATACATA-TTTTGTGTATCGATACA
1 TGTATCGATACATATTTTTGTGTATCGATACA
545558 AGTTTGGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 17 0.55
34 14 0.45
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATATTTTTGTGTATCGATACAT
Found at i:545551 original size:19 final size:19
Alignment explanation
Indices: 545493--545557 Score: 70
Period size: 19 Copynumber: 3.6 Consensus size: 19
545483 TACAAGCCAA
545493 TGTATCGATACATATTTTTTG
1 TGTATCGATACATA--TTTTG
545514 TGTATCGATAC--A---T-
1 TGTATCGATACATATTTTG
545527 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
545546 TGTATCGATACA
1 TGTATCGATACA
545558 AGTTTGGCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
15 1 0.03
18 1 0.03
19 13 0.34
21 11 0.29
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:548106 original size:13 final size:13
Alignment explanation
Indices: 548088--548123 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
548078 ATAATCCCCC
548088 TGTATCGATACAG
1 TGTATCGATACAG
*
548101 TGTATCGATACAT
1 TGTATCGATACAG
*
548114 TGTATTGATA
1 TGTATCGATA
548124 TAAAGAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:550227 original size:15 final size:15
Alignment explanation
Indices: 550207--550237 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
550197 ATTTCGTTTG
*
550207 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
550222 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
550237 G
1 G
550238 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:552069 original size:21 final size:21
Alignment explanation
Indices: 552040--552084 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
552030 AAGTTTTTAT
*
552040 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
552060 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
552082 TTT
1 TTT
552085 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:554325 original size:13 final size:13
Alignment explanation
Indices: 554307--554332 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
554297 ATATTTTTTG
554307 TGTATCGATACAT
1 TGTATCGATACAT
554320 TGTATCGATACAT
1 TGTATCGATACAT
554333 ATTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:554343 original size:32 final size:33
Alignment explanation
Indices: 554286--554350 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
554276 TACAAGCCAA
*
554286 TGTATCGATACATATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-TTTTTGTGTATCAATACAT
554320 TGTATCGATACATA-TTTTGTGTATCAATACA
1 TGTATCGATACATATTTTTGTGTATCAATACA
554351 AGTTTGGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 16 0.53
34 14 0.47
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATATTTTTGTGTATCAATACAT
Found at i:554344 original size:19 final size:19
Alignment explanation
Indices: 554286--554350 Score: 61
Period size: 19 Copynumber: 3.6 Consensus size: 19
554276 TACAAGCCAA
554286 TGTATCGATACATATTTTTTG
1 TGTATCGATACATA--TTTTG
554307 TGTATCGATAC--A---T-
1 TGTATCGATACATATTTTG
554320 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
*
554339 TGTATCAATACA
1 TGTATCGATACA
554351 AGTTTGGCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 14
0.71 0.02 0.27
Matches are distributed among these distances:
13 11 0.30
14 1 0.03
15 1 0.03
18 1 0.03
19 12 0.32
21 11 0.30
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:556884 original size:21 final size:20
Alignment explanation
Indices: 556858--556911 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
556848 ACAGGGTCCA
556858 GTATCGATACATTGCAAGCAT
1 GTATCGATACATT-CAAGCAT
**
556879 GTATCGATACATTCAATTAT
1 GTATCGATACATTCAAGCAT
556899 GTATCGATACATT
1 GTATCGATACATT
556912 AACTTATTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 18 0.58
21 13 0.42
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (20 bp):
GTATCGATACATTCAAGCAT
Found at i:556924 original size:21 final size:20
Alignment explanation
Indices: 556858--556930 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 20
556848 ACAGGGTCCA
**
556858 GTATCGATACATTGCAAGCAT
1 GTATCGATACATT-CAATTAT
556879 GTATCGATACATTCAATTAT
1 GTATCGATACATTCAATTAT
556899 GTATCGATACATT-AACTTATT
1 GTATCGATACATTCAA-TTA-T
556920 GTATCGATACA
1 GTATCGATACA
556931 AATTATAGAA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.04
20 21 0.44
21 25 0.52
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (20 bp):
GTATCGATACATTCAATTAT
Found at i:558254 original size:49 final size:49
Alignment explanation
Indices: 558199--558297 Score: 137
Period size: 49 Copynumber: 2.0 Consensus size: 49
558189 ATGACAAGCT
* *
558199 ATTAATATAGCTTTTCTCTAAAAACCTTGTTTAATACT-AAAATATGATA
1 ATTAATATAGCTTTTCTCCAAAAACCTTGTCTAATA-TAAAAATATGATA
** *
558248 ATTAATATAGCTTTTCTCCGTAAGCCTTGTCTAATATAAAAATATGATA
1 ATTAATATAGCTTTTCTCCAAAAACCTTGTCTAATATAAAAATATGATA
558297 A
1 A
558298 CAATGAATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
48 1 0.02
49 43 0.98
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.39
Consensus pattern (49 bp):
ATTAATATAGCTTTTCTCCAAAAACCTTGTCTAATATAAAAATATGATA
Found at i:558499 original size:15 final size:15
Alignment explanation
Indices: 558476--558505 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
558466 ATAGTGAAGT
558476 TAAACTTTAAATTTA
1 TAAACTTTAAATTTA
*
558491 TAAATTTTAAATTTA
1 TAAACTTTAAATTTA
558506 CCAATCTATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
TAAACTTTAAATTTA
Found at i:558835 original size:18 final size:18
Alignment explanation
Indices: 558812--558846 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
558802 AACAACATTT
558812 TTCTTCTTCTTGTTCTTA
1 TTCTTCTTCTTGTTCTTA
*
558830 TTCTTCTTGTTGTTCTT
1 TTCTTCTTCTTGTTCTT
558847 TTCCTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.03, C:0.20, G:0.09, T:0.69
Consensus pattern (18 bp):
TTCTTCTTCTTGTTCTTA
Found at i:558857 original size:3 final size:3
Alignment explanation
Indices: 558851--558900 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
558841 GTTCTTTTCC
*
558851 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TGA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
558899 TT
1 TT
558901 GAGTTTATAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:559416 original size:32 final size:32
Alignment explanation
Indices: 559348--559416 Score: 75
Period size: 32 Copynumber: 2.2 Consensus size: 32
559338 ACCCTAAGTC
* * ** *
559348 AATTGTATCAATACATTATGCCTGACAGCTAT
1 AATTTTATCAATACATTAAGCCCAACAGCTAG
* *
559380 AATTTTATCGATACATTAAGCCCAACGGCTAG
1 AATTTTATCAATACATTAAGCCCAACAGCTAG
559412 AATTT
1 AATTT
559417 CAAATGCATT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (32 bp):
AATTTTATCAATACATTAAGCCCAACAGCTAG
Found at i:562712 original size:13 final size:13
Alignment explanation
Indices: 562694--562721 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
562684 ATACAAAGAT
562694 CAATGTATCGATA
1 CAATGTATCGATA
562707 CAATGTATCGATA
1 CAATGTATCGATA
562720 CA
1 CA
562722 TTTGAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:562799 original size:33 final size:33
Alignment explanation
Indices: 562762--562828 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
562752 AGTAGCTTAA
562762 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
562795 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
562828 A
1 A
562829 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:562802 original size:13 final size:13
Alignment explanation
Indices: 562784--562808 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
562774 CAAAAAAATA
562784 TGTATCGATACAT
1 TGTATCGATACAT
562797 TGTATCGATACA
1 TGTATCGATACA
562809 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:564505 original size:3 final size:3
Alignment explanation
Indices: 564497--564551 Score: 101
Period size: 3 Copynumber: 18.3 Consensus size: 3
564487 TGAACCATCA
*
564497 ATG ATG ATG AAG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
564545 ATG ATG A
1 ATG ATG A
564552 GGTTGACTTG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.36, C:0.00, G:0.33, T:0.31
Consensus pattern (3 bp):
ATG
Found at i:569541 original size:49 final size:49
Alignment explanation
Indices: 569381--570381 Score: 841
Period size: 49 Copynumber: 20.8 Consensus size: 49
569371 CGAAGAATGA
* * * ** *
569381 CAATGTGCTGATTCATGGCCAGCGACATTAGACTTGCAGAAGAA--TGC
1 CAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
** * * * * * * *
569428 CAATGTGCTGAGACAAGACCAACGACATTGGGCTTAGGAATGTTAAAGATGC
1 CAATGTGCTGATTCAAGGCCAGCGATATTGGACTTA--AA-GATGAAGGTGC
** * * * *
569480 CAATACGCTGATTCAAGGCCAACGATATTGGACTTAAAGCTGAAGATAC
1 CAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
* * * **
569529 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAATATGACGAAGGCAC
1 CAATGTGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A-GATGAAGGTGC
* *
569581 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
* * * *
569630 CAATGTACTAATTCAAGGCCAGCGACATTGGACTTAAAAATGACAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG---AAGGTGC
* ** * *
569682 CAATATGCTGATTCAAGGCCAGCGATATCAGACTTAAAGCTGAAGATGC
1 CAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
* * * * * **
569731 CAATGTGCTGATTCAAGGCCGGTGACATTTGTCTTAAAGATGACAAAGGCAC
1 CAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG---AAGGTGC
* * * *
569783 CACTATGCTAATTCAAGGGCAGCGATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
* * ***
569832 CAATGTACTGATTCAAGGCCAGCGACATTGGACTTAAAGATGATAAAAACGC
1 CAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG---AAGGTGC
* *
569884 CAATATGCTGATTCAAGGCGAGCGATATTGGAC-T-----T----GTGC
1 CAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
* * * *
569923 CAATGTGCTGCTTCAAGGCCAGCGACATTGGTCTTAAAGA-CAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
* *
569971 CAATATGCTGATTCAAGGCCAGCGATATTGGGC-T-----T----GTGC
1 CAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
* **
570010 CAATGTGCTGATTCAAGGCCAGCGACATTGGTTTTAAAGAT-AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
* * *
570058 CAATATGCTGATTCAAGGCCAGTGATATTGGGGC-T-----T----GTGC
1 CAATGTGCTGATTCAAGGCCAGCGATATT-GGACTTAAAGATGAAGGTGC
* ** * *
570098 CAATGTGCTGATTCAAGGTCAATGACATTGGTCTTAAAGAT-AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
* * *
570146 CAATATGCTGATTCAAGGCTAGCGATATTTGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
* * *
570195 CAATATGCTGATTTAAGGCCAGCGATATTGGACTTAAAGATGAAGGTCC
1 CAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
570244 CAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
* * *
570293 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA-CAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
* * *
570341 CAATATGCTGATTCAAGGCTAGCGATATTGGGCTTAGAAGA
1 CAATGTGCTGATTCAAGGCCAGCGATATTGGACTTA-AAGA
570382 ATACGCCACC
Statistics
Matches: 770, Mismatches: 135, Indels: 96
0.77 0.13 0.10
Matches are distributed among these distances:
39 66 0.09
40 32 0.04
43 1 0.00
45 2 0.00
46 1 0.00
47 29 0.04
48 140 0.18
49 305 0.40
50 8 0.01
51 4 0.01
52 182 0.24
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
Found at i:569584 original size:101 final size:98
Alignment explanation
Indices: 569381--570381 Score: 985
Period size: 101 Copynumber: 10.4 Consensus size: 98
569371 CGAAGAATGA
* * * * ** * **
569381 CAATGTGCTGATTCATGGCCAGCGACATTAGACTTGCAGAAGAA--TGCCAATGTGCTGAGACAA
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAA
* * * ** *
569444 GACCAACGACATTGGGCTTAGGAATGTTAAAGATGC
66 GGCCAGCGACATTGGTCTTA--AA-GACAAAGGTGC
* * * * *
569480 CAATACGCTGATTCAAGGCCAACGATATTGGACTTAAAGCTGAAGATACCAATGTGCTGATTCAA
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAA
* **
569545 GGCCAGCGACATTGGTCTTAAATATGACGAAGGCAC
66 GGCCAGCGACATTGGTCTT-AA-A-GACAAAGGTGC
* * *
569581 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATAAAGGTGCCAATGTACTAATTCAA
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAA
*
569646 GGCCAGCGACATTGGACTTAAAAATGACAAAGGTGC
66 GGCCAGCGACATTGGTCTT--AAA-GACAAAGGTGC
** * *
569682 CAATATGCTGATTCAAGGCCAGCGATATCAGACTTAAAGCTGAAGATGCCAATGTGCTGATTCAA
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAA
* * * **
569747 GGCCGGTGACATTTGTCTTAAAGATGACAAAGGCAC
66 GGCCAGCGACATTGGTCTT-AA-A-GACAAAGGTGC
* * * *
569783 CACTATGCTAATTCAAGGGCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTACTGATTCAA
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAA
* * ***
569848 GGCCAGCGACATTGGACTTAAAGATGATAAAAACGC
66 GGCCAGCGACATTGGTCTT-AA-A-GACAAAGGTGC
* *
569884 CAATATGCTGATTCAAGGCGAGCGATATTGGAC-T-----T----GTGCCAATGTGCTGCTTCAA
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAA
569939 GGCCAGCGACATTGGTCTTAAAGAC-AAGGTGC
66 GGCCAGCGACATTGGTCTTAAAGACAAAGGTGC
*
569971 CAATATGCTGATTCAAGGCCAGCGATATTGGGC-T-----T----GTGCCAATGTGCTGATTCAA
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAA
* *
570026 GGCCAGCGACATTGGTTTTAAAGA-TAAGGTGC
66 GGCCAGCGACATTGGTCTTAAAGACAAAGGTGC
* *
570058 CAATATGCTGATTCAAGGCCAGTGATATTGGGGC-T-----T----GTGCCAATGTGCTGATTCA
1 CAATATGCTGATTCAAGGCCAGCGATATT-GGACTTAAAGATGAAGGTGCCAATGTGCTGATTCA
* ** *
570113 AGGTCAATGACATTGGTCTTAAAGA-TAAGGTGC
65 AGGCCAGCGACATTGGTCTTAAAGACAAAGGTGC
* * * *
570146 CAATATGCTGATTCAAGGCTAGCGATATTTGACTTAAAGATGAAGGTGCCAATATGCTGATTTAA
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAA
* * ** *
570211 GGCCAGCGATATTGGACTTAAAGATGAAGGTCC
66 GGCCAGCGACATTGGTCTTAAAGACAAAGGTGC
*
570244 CAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAA
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAA
570309 GGCCAGCGACATTGGTCTTAAAGAC-AAGGTGC
66 GGCCAGCGACATTGGTCTTAAAGACAAAGGTGC
* *
570341 CAATATGCTGATTCAAGGCTAGCGATATTGGGCTTAGAAGA
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTA-AAGA
570382 ATACGCCACC
Statistics
Matches: 774, Mismatches: 108, Indels: 41
0.84 0.12 0.04
Matches are distributed among these distances:
87 116 0.15
88 84 0.11
89 1 0.00
90 2 0.00
91 36 0.05
93 1 0.00
95 1 0.00
97 76 0.10
98 92 0.12
99 34 0.04
100 5 0.01
101 322 0.42
102 4 0.01
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (98 bp):
CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAA
GGCCAGCGACATTGGTCTTAAAGACAAAGGTGC
Found at i:569938 original size:39 final size:39
Alignment explanation
Indices: 569882--570115 Score: 171
Period size: 39 Copynumber: 5.5 Consensus size: 39
569872 TGATAAAAAC
* *
569882 GCCAATATGCTGATTCAAGGCGAGCGATATTGGACTTGT
1 GCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTGT
* * *
569921 GCCAATGTGCTGCTTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGT
1 GCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT---------GT
* *
569969 GCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTGT
1 GCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTGT
* * *
570008 GCCAATGTGCTGATTCAAGGCCAGCGACATTGGTTTTAAAGATAAGGT
1 GCCAATATGCTGATTCAAGGCCAGCGACATTGG------A-CT--TGT
* * *
570056 GCCAATATGCTGATTCAAGGCCAGTGATATTGGGGCTTGT
1 GCCAATATGCTGATTCAAGGCCAGCGACATT-GGACTTGT
*
570096 GCCAATGTGCTGATTCAAGG
1 GCCAATATGCTGATTCAAGG
570116 TCAATGACAT
Statistics
Matches: 155, Mismatches: 21, Indels: 37
0.73 0.10 0.17
Matches are distributed among these distances:
39 65 0.42
40 21 0.14
42 1 0.01
46 1 0.01
48 65 0.42
49 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.27
Consensus pattern (39 bp):
GCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTGT
Found at i:570008 original size:87 final size:87
Alignment explanation
Indices: 569828--570371 Score: 611
Period size: 87 Copynumber: 6.0 Consensus size: 87
569818 AAAGATGAAG
* * * ***
569828 GTGCCAATGTACTGATTCAAGGCCAGCGACATTGGACTTAAAGATGATAAAAACGCCAATATGCT
1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT-AA-A-GA-CAAGGTGCCAATATGCT
*
569893 GATTCAAGGCGAGCGATATTGGACTT
62 GATTCAAGGCCAGCGATATTGGACTT
*
569919 GTGCCAATGTGCTGCTTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
*
569984 CAAGGCCAGCGATATTGGGCTT
66 CAAGGCCAGCGATATTGGACTT
* *
570006 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTTTTAAAGATAAGGTGCCAATATGCTGATT
1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
* *
570071 CAAGGCCAGTGATATTGGGGCTT
66 CAAGGCCAGCGATATT-GGACTT
* ** *
570094 GTGCCAATGTGCTGATTCAAGGTCAATGACATTGGTCTTAAAGATAAGGTGCCAATATGCTGATT
1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
* *
570159 CAAGGCTAGCGATATTTGACTTAAAGAT
66 CAAGGCCAGCGATATTGGAC-T-----T
* * * * * * *
570187 GAAGGTGCCAATATGCTGATTTAAGGCCAGCGATATTGGACTTAAAGATGAAGGTCCCAATGTGC
1 ----GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA-CAAGGTGCCAATATGC
570252 TGATTCAAGGCCAGCGATATTGGACTTAAAGAT
61 TGATTCAAGGCCAGCGATATTGGAC-T-----T
570285 GAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCT
1 ----GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCT
*
570350 GATTCAAGGCTAGCGATATTGG
62 GATTCAAGGCCAGCGATATTGG
570372 GCTTAGAAGA
Statistics
Matches: 400, Mismatches: 41, Indels: 18
0.87 0.09 0.04
Matches are distributed among these distances:
87 116 0.29
88 84 0.21
89 1 0.00
90 2 0.00
91 36 0.09
93 1 0.00
97 72 0.18
98 88 0.22
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.26
Consensus pattern (87 bp):
GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
CAAGGCCAGCGATATTGGACTT
Found at i:570456 original size:28 final size:29
Alignment explanation
Indices: 570398--570550 Score: 176
Period size: 28 Copynumber: 5.3 Consensus size: 29
570388 CACCAACTTG
570398 TGTGGGCTTTTGAAAGGGTTG-CACCA-ACT
1 TGTGGGCTTTTG-AAGGGTTGCCA-CAGACT
*
570427 TGTGTGCTTTTGAA-GGTTGCCACAGACT
1 TGTGGGCTTTTGAAGGGTTGCCACAGACT
570455 TGTGGGCTTTTGAA-GGTTGCCACAGACT
1 TGTGGGCTTTTGAAGGGTTGCCACAGACT
* *
570483 TGTGGGC-TTTGAAAGGGGTGCCACCGACT
1 TGTGGGCTTTTG-AAGGGTTGCCACAGACT
570512 TGTGGGCTTTTGAAAAGGG-TGCCATC-GACT
1 TGTGGGCTTTTG--AAGGGTTGCCA-CAGACT
570542 TGTGGGCTT
1 TGTGGGCTT
570551 AAAAGGAGAA
Statistics
Matches: 113, Mismatches: 4, Indels: 13
0.87 0.03 0.10
Matches are distributed among these distances:
27 11 0.10
28 43 0.38
29 30 0.27
30 22 0.19
31 7 0.06
ACGTcount: A:0.18, C:0.18, G:0.33, T:0.31
Consensus pattern (29 bp):
TGTGGGCTTTTGAAGGGTTGCCACAGACT
Found at i:570505 original size:57 final size:57
Alignment explanation
Indices: 570398--570550 Score: 181
Period size: 57 Copynumber: 2.7 Consensus size: 57
570388 CACCAACTTG
* *
570398 TGTGGGCTTTTGAAAGGGTTG-CACCA-ACTTGTGTGCTTTTGAAGGTTGCCACAGACT
1 TGTGGGCTTTTGAAA-GGTTGCCACCAGACTTGTGGGC-TTTGAAGGGTGCCACAGACT
*
570455 TGTGGGCTTTTG-AAGGTTGCCA-CAGACTTGTGGGCTTTGAAAGGGGTGCCACCGACT
1 TGTGGGCTTTTGAAAGGTTGCCACCAGACTTGTGGGCTTTG-AA-GGGTGCCACAGACT
* *
570512 TGTGGGCTTTTGAAAAGGGTGCCATC-GACTTGTGGGCTT
1 TGTGGGCTTTTG-AAAGGTTGCCACCAGACTTGTGGGCTT
570551 AAAAGGAGAA
Statistics
Matches: 85, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
55 11 0.13
56 15 0.18
57 36 0.42
59 22 0.26
60 1 0.01
ACGTcount: A:0.18, C:0.18, G:0.33, T:0.31
Consensus pattern (57 bp):
TGTGGGCTTTTGAAAGGTTGCCACCAGACTTGTGGGCTTTGAAGGGTGCCACAGACT
Found at i:570585 original size:33 final size:32
Alignment explanation
Indices: 570541--570684 Score: 136
Period size: 33 Copynumber: 4.5 Consensus size: 32
570531 TGCCATCGAC
*
570541 TTGTGGGCTTAAAAGGAGAAAGATGCCACGGAG
1 TTGTGGACTTAAAAGGA-AAAGATGCCACGGAG
* *
570574 TGGTGGACTTAAAAGGAAACAGATGCCACAGAG
1 TTGTGGACTTAAAAGGAAA-AGATGCCACGGAG
* * *
570607 TTGTGGGCTTTAAAAAGAAAAAATGTGCCACGGAG
1 TTGTGGAC-TTAAAAGGAAAAGA--TGCCACGGAG
* *
570642 TTGTGGACTTACAAGG----G-TGCCACAGAG
1 TTGTGGACTTAAAAGGAAAAGATGCCACGGAG
570669 TTGTGGACTTAAAAGG
1 TTGTGGACTTAAAAGG
570685 GTGCCACGAA
Statistics
Matches: 93, Mismatches: 14, Indels: 14
0.77 0.12 0.12
Matches are distributed among these distances:
27 24 0.26
32 2 0.02
33 35 0.38
34 16 0.17
35 16 0.17
ACGTcount: A:0.34, C:0.13, G:0.32, T:0.21
Consensus pattern (32 bp):
TTGTGGACTTAAAAGGAAAAGATGCCACGGAG
Found at i:570669 original size:27 final size:27
Alignment explanation
Indices: 570631--570793 Score: 157
Period size: 27 Copynumber: 5.8 Consensus size: 27
570621 AAGAAAAAAT
* *
570631 GTGCCACGGAGTTGTGGACTTACAAGG
1 GTGCCACAGAGTTGTGGACTTAAAAGG
570658 GTGCCACAGAGTTGTGGACTTAAAAGG
1 GTGCCACAGAGTTGTGGACTTAAAAGG
* *
570685 GTGCCAC-GAAATTGTGGACTTAAAAAAAAAAAAG
1 GTGCCACAG-AGTTGTGGACTT-------AAAAGG
* * * *
570719 GTGCCGCGGGGTTGTGGACTCAAAAGG
1 GTGCCACAGAGTTGTGGACTTAAAAGG
*
570746 GTGTCACAGAGTTGTGGACTTAAAAGG
1 GTGCCACAGAGTTGTGGACTTAAAAGG
*
570773 GTGCCACAGAGTCGTGGACTT
1 GTGCCACAGAGTTGTGGACTT
570794 TTGGAAAAGA
Statistics
Matches: 111, Mismatches: 16, Indels: 18
0.77 0.11 0.12
Matches are distributed among these distances:
26 1 0.01
27 89 0.80
34 20 0.18
35 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.33, T:0.21
Consensus pattern (27 bp):
GTGCCACAGAGTTGTGGACTTAAAAGG
Found at i:570790 original size:88 final size:88
Alignment explanation
Indices: 570597--570793 Score: 279
Period size: 88 Copynumber: 2.2 Consensus size: 88
570587 AGGAAACAGA
* * * * *
570597 TGCCACAGAGTTGTGGGCTTTAAAAAGAAAAAATGTGCCACGGAGTTGTGGACTTACAAGGGTGC
1 TGCCACAGAGTTGTGGAC-TTAAAAAAAAAAAAGGTGCCACGGAGTTGTGGACTCAAAAGGGTGC
570662 CACAGAGTTGTGGACTTAAAAGGG
65 CACAGAGTTGTGGACTTAAAAGGG
* * * *
570686 TGCCAC-GAAATTGTGGACTTAAAAAAAAAAAAGGTGCCGCGGGGTTGTGGACTCAAAAGGGTGT
1 TGCCACAG-AGTTGTGGACTTAAAAAAAAAAAAGGTGCCACGGAGTTGTGGACTCAAAAGGGTGC
570750 CACAGAGTTGTGGACTTAAAAGGG
65 CACAGAGTTGTGGACTTAAAAGGG
*
570774 TGCCACAGAGTCGTGGACTT
1 TGCCACAGAGTTGTGGACTT
570794 TTGGAAAAGA
Statistics
Matches: 95, Mismatches: 11, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
88 80 0.84
89 15 0.16
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.22
Consensus pattern (88 bp):
TGCCACAGAGTTGTGGACTTAAAAAAAAAAAAGGTGCCACGGAGTTGTGGACTCAAAAGGGTGCC
ACAGAGTTGTGGACTTAAAAGGG
Found at i:570902 original size:63 final size:63
Alignment explanation
Indices: 570774--570995 Score: 250
Period size: 63 Copynumber: 3.5 Consensus size: 63
570764 CTTAAAAGGG
* * * * * * **
570774 TGCCACAGAGTCGTGGACTTTTGGAAA-AGATGCTATTAAGTTGTGGA-TATTGAAGAAAAAAGA
1 TGCCACTGAGTCATGGACTTTGGGAAAGAGATGCCACTGAGTCATGGACT-TTGAAG-AAAAAGA
* * *
570837 TGCCACTAAGTTATGGACTTTGGGAAAGAGATGCCACTGAGTCATGGACTTTGAAGAAAAGGA
1 TGCCACTGAGTCATGGACTTTGGGAAAGAGATGCCACTGAGTCATGGACTTTGAAGAAAAAGA
* * * **
570900 TGCCATTGAGTCGTGGACTTTGGGAAACAGATGCCACTGAGTTGTGGACTTTGAAGAAAAAGA
1 TGCCACTGAGTCATGGACTTTGGGAAAGAGATGCCACTGAGTCATGGACTTTGAAGAAAAAGA
*
570963 TGCCACTGAGTCATGGACTTTGAGAAGAGAGAT
1 TGCCACTGAGTCATGGACTTTGGGAA-AGAGAT
570996 TTGAAGAATT
Statistics
Matches: 133, Mismatches: 23, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
63 106 0.80
64 26 0.20
65 1 0.01
ACGTcount: A:0.33, C:0.13, G:0.29, T:0.25
Consensus pattern (63 bp):
TGCCACTGAGTCATGGACTTTGGGAAAGAGATGCCACTGAGTCATGGACTTTGAAGAAAAAGA
Found at i:570910 original size:32 final size:32
Alignment explanation
Indices: 570823--570985 Score: 204
Period size: 32 Copynumber: 5.1 Consensus size: 32
570813 GTTGTGGATA
* *
570823 TTGAAGAAAAAAGATGCCACTAAGTTATGGACT
1 TTGAAG-AAAAAGATGCCACTGAGTCATGGACT
* *
570856 TTG-GGAAAGAGATGCCACTGAGTCATGGACT
1 TTGAAGAAAAAGATGCCACTGAGTCATGGACT
* * *
570887 TTGAAGAAAAGGATGCCATTGAGTCGTGGACT
1 TTGAAGAAAAAGATGCCACTGAGTCATGGACT
* * **
570919 TTG-GGAAACAGATGCCACTGAGTTGTGGACT
1 TTGAAGAAAAAGATGCCACTGAGTCATGGACT
570950 TTGAAGAAAAAGATGCCACTGAGTCATGGACT
1 TTGAAGAAAAAGATGCCACTGAGTCATGGACT
570982 TTGA
1 TTGA
570986 GAAGAGAGAT
Statistics
Matches: 110, Mismatches: 18, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
31 52 0.47
32 55 0.50
33 3 0.03
ACGTcount: A:0.33, C:0.14, G:0.28, T:0.25
Consensus pattern (32 bp):
TTGAAGAAAAAGATGCCACTGAGTCATGGACT
Found at i:586666 original size:26 final size:26
Alignment explanation
Indices: 586615--586685 Score: 74
Period size: 26 Copynumber: 2.7 Consensus size: 26
586605 AACAAAATTG
* *
586615 TTGTCAAGAAAT-TTTCGTCAAGAACTT
1 TTGTCAAGAAATGTGT-GTCAAAAAC-T
*
586642 TTGTCGAG-AATGTGTGTCAAAAACT
1 TTGTCAAGAAATGTGTGTCAAAAACT
*
586667 TTGTCAAGAAATGTTTGTC
1 TTGTCAAGAAATGTGTGTC
586686 GACACGAATC
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
25 8 0.22
26 20 0.54
27 9 0.24
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.37
Consensus pattern (26 bp):
TTGTCAAGAAATGTGTGTCAAAAACT
Found at i:586685 original size:14 final size:13
Alignment explanation
Indices: 586609--586685 Score: 68
Period size: 14 Copynumber: 5.8 Consensus size: 13
586599 ATTGTCAACA
586609 AAATTGTTGTCAAG
1 AAATT-TTGTCAAG
586623 AAATTTTCGTCAAG
1 AAATTTT-GTCAAG
* *
586637 AACTTTTGTCGAG
1 AAATTTTGTCAAG
*
586650 -AATGTGTGTCAA-
1 AAAT-TTTGTCAAG
*
586662 AAACTTTGTCAAG
1 AAATTTTGTCAAG
586675 AAATGTTTGTC
1 AAAT-TTTGTC
586686 GACACGAATC
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
12 9 0.18
13 18 0.36
14 23 0.46
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.36
Consensus pattern (13 bp):
AAATTTTGTCAAG
Found at i:586749 original size:28 final size:28
Alignment explanation
Indices: 586708--586775 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 28
586698 TTCTGAAAGC
* *
586708 CCACTAGTCAGTGGCACCTCTTCGAAGT
1 CCACAAGTTAGTGGCACCTCTTCGAAGT
* * *
586736 CCACAAGTTAGTGGTATCTCTTTGAAGT
1 CCACAAGTTAGTGGCACCTCTTCGAAGT
586764 CCACAA-TTAGTG
1 CCACAAGTTAGTG
586776 ACACTTGTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
27 6 0.17
28 29 0.83
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (28 bp):
CCACAAGTTAGTGGCACCTCTTCGAAGT
Found at i:587044 original size:32 final size:32
Alignment explanation
Indices: 586950--587057 Score: 119
Period size: 32 Copynumber: 3.4 Consensus size: 32
586940 CCTAGTGGAG
* *
586950 AACCCTTTTTAAAGCCTACACAAGTCGGTGAC
1 AACCCTTTCTAAAGCCTACACAAGTCGGTGGC
* *
586982 AACCC-TTCTTAAAGCCTACACTAGTCGGTGGT
1 AACCCTTTC-TAAAGCCTACACAAGTCGGTGGC
* * *
587014 AACCCTTTCAAAAGCCCACACAAGTTGGTGGC
1 AACCCTTTCTAAAGCCTACACAAGTCGGTGGC
* *
587046 ATCTCTTTCTAA
1 AACCCTTTCTAA
587058 GTCTAATATC
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
31 2 0.03
32 57 0.92
33 3 0.05
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.27
Consensus pattern (32 bp):
AACCCTTTCTAAAGCCTACACAAGTCGGTGGC
Found at i:587109 original size:43 final size:43
Alignment explanation
Indices: 587055--587142 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 43
587045 CATCTCTTTC
* * * *
587055 TAAGTCTAATATCGTTGGCCTTGAATCAACACATTGGCACCTT
1 TAAGTCCAATATCGCTAGCCTTGAATCAACACATTGACACCTT
* *
587098 TAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGACACCTT
1 TAAGTCCAATATCGCTAGCCTTGAATCAACACATTGACACCTT
587141 TA
1 TA
587143 TCATCCTTCT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.32
Consensus pattern (43 bp):
TAAGTCCAATATCGCTAGCCTTGAATCAACACATTGACACCTT
Found at i:587289 original size:52 final size:52
Alignment explanation
Indices: 587233--587659 Score: 178
Period size: 52 Copynumber: 8.1 Consensus size: 52
587223 CACTGACCTC
* *
587233 GAATCAGCACATTGGCATTCTTCTCATCTTCAAGTCAAATGTTGCTGG-TTGT
1 GAATCAGCACATTGGCATTCTTATCATCTTCAAGTCCAATGTTGCTGGCTT-T
* * * * * *
587285 GAATCAACGCATTGACATTC--ATCACCTTCAAGTCCAATTTTGCTGGCCTT
1 GAATCAGCACATTGGCATTCTTATCATCTTCAAGTCCAATGTTGCTGGCTTT
* * * * *
587335 GAATCAGTATATTGGCA-CCTTTATCATCTTTAAGTCCAATGTTACTGGCCTTT
1 GAATCAGCACATTGGCATTC-TTATCATCTTCAAGTCCAATGTTGCTGG-CTTT
* * ** * * *
587388 -AATCAGCACATTGGTACCTT-TT-TC-TTTCTCAAGTCCAACATCGCTAGCCTT
1 GAATCAGCACATTGG--CATTCTTATCATCT-TCAAGTCCAATGTTGCTGGCTTT
* * * * *** * *
587439 GAATTAGCATC-TTGGCACTT-TTATCATCTTTAAGCCCAACGTCATTGACCTT
1 GAATCAGCA-CATTGGCA-TTCTTATCATCTTCAAGTCCAATGTTGCTGGCTTT
* * * *
587491 GAATCAGCACTTTGGCACTTTTCCACCTTTATCATCTTTAAGTCCAATGTTGTTGGCCTT
1 GAATCAGCACATTGGCA---TT----C-TTATCATCTTCAAGTCCAATGTTGCTGGCTTT
* * * ** * *
587551 GAATCAGCATATTGGCACCTTCTTCT-TTC-TCAAGTCCAACATCGCTGGCCTT
1 GAATCAGCACATTGGCA--TTCTTATCATCTTCAAGTCCAATGTTGCTGGCTTT
* * * * * *
587603 GAATCAACATATTGGCACTT-TTATCATCTTTAAGTCCAGTGTTGCAGGCCTT
1 GAATCAGCACATTGGCA-TTCTTATCATCTTCAAGTCCAATGTTGCTGGCTTT
587655 GAATC
1 GAATC
587660 TACACGCTGG
Statistics
Matches: 282, Mismatches: 68, Indels: 50
0.70 0.17 0.12
Matches are distributed among these distances:
49 1 0.00
50 39 0.14
51 16 0.06
52 165 0.59
53 10 0.04
54 6 0.02
55 1 0.00
59 2 0.01
60 42 0.15
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.36
Consensus pattern (52 bp):
GAATCAGCACATTGGCATTCTTATCATCTTCAAGTCCAATGTTGCTGGCTTT
Found at i:587462 original size:104 final size:104
Alignment explanation
Indices: 587312--587505 Score: 253
Period size: 104 Copynumber: 1.9 Consensus size: 104
587302 TTCATCACCT
** * * * * *
587312 TCAAGTCCAATTTTGCTGGCCTTGAATCAGTATATTGGCACCTTTATCATCTTTAAGTCCAATGT
1 TCAAGTCCAACATCGCTAGCCTTGAATCAGCATATTGGCACCTTTATCATCTTTAAGCCCAACGT
* * *
587377 TACTGGCCTTTAATCAGCACATTGGTACCTTTTTCTTTC
66 CACTGACCTTGAATCAGCACATTGGTACCTTTTTCTTTC
* * *
587416 TCAAGTCCAACATCGCTAGCCTTGAATTAGCATCTTGGCACTTTTATCATCTTTAAGCCCAACGT
1 TCAAGTCCAACATCGCTAGCCTTGAATCAGCATATTGGCACCTTTATCATCTTTAAGCCCAACGT
* *
587481 CATTGACCTTGAATCAGCACTTTGG
66 CACTGACCTTGAATCAGCACATTGG
587506 CACTTTTCCA
Statistics
Matches: 75, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
104 75 1.00
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.37
Consensus pattern (104 bp):
TCAAGTCCAACATCGCTAGCCTTGAATCAGCATATTGGCACCTTTATCATCTTTAAGCCCAACGT
CACTGACCTTGAATCAGCACATTGGTACCTTTTTCTTTC
Found at i:588239 original size:21 final size:20
Alignment explanation
Indices: 588218--588255 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
588208 CGTTTTTTAT
*
588218 TTAAATGTATCGCTACATTA
1 TTAAATGTATCGATACATTA
*
588238 TTCAATGTATCGATACAT
1 TTAAATGTATCGATACAT
588256 GAAGGTAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (20 bp):
TTAAATGTATCGATACATTA
Found at i:588577 original size:104 final size:104
Alignment explanation
Indices: 588379--588648 Score: 335
Period size: 104 Copynumber: 2.6 Consensus size: 104
588369 GCACTCTTCT
* * * *
588379 CACCTTTATCATCTTTAAGTCTAATGTTGCTGGG-CTTGAATCAGCACATTGGCACCTTTTTCTT
1 CACCTTTATCATCTTTAAGACCAATGTTGC-GGGCCTTGAATCAGCACATTAGCACCTTCTTCTT
* * *
588443 TCTTAAGTCCAACATCGTTGGCCTTGAATCAACATATTGG
65 TCTCAAGTCCAACATCGCTGGCCTTAAATCAACATATTGG
*
588483 CACTTTTATCATCTTTAAGACCAATGTTGCGGGCCTTGAATCAGCACATTAGCACCTTCTTCTTT
1 CACCTTTATCATCTTTAAGACCAATGTTGCGGGCCTTGAATCAGCACATTAGCACCTTCTTCTTT
* * **
588548 CTCAAGTCCAACATTGCTGGCTTTAAATCAGTATATTGG
66 CTCAAGTCCAACATCGCTGGCCTTAAATCAACATATTGG
* * * * * * * *
588587 CACCTCTATCATCTTTAAGCCCAACGTCGCTGACCTTGAATTAGCACTTTAGCACTCTTCTT
1 CACCTTTATCATCTTTAAGACCAATGTTGCGGGCCTTGAATCAGCACATTAGCAC-CTTCTT
588649 ATCTTTATCG
Statistics
Matches: 143, Mismatches: 21, Indels: 3
0.86 0.13 0.02
Matches are distributed among these distances:
103 3 0.02
104 134 0.94
105 6 0.04
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.36
Consensus pattern (104 bp):
CACCTTTATCATCTTTAAGACCAATGTTGCGGGCCTTGAATCAGCACATTAGCACCTTCTTCTTT
CTCAAGTCCAACATCGCTGGCCTTAAATCAACATATTGG
Found at i:588611 original size:52 final size:52
Alignment explanation
Indices: 588379--588633 Score: 212
Period size: 52 Copynumber: 4.9 Consensus size: 52
588369 GCACTCTTCT
* ** *
588379 CACCTTTATCATCTTTAAGTCTAATGTTGCTGGGCTTGAATCAGCACATTGG
1 CACCTTTATCATCTTTAAGTCCAACATTGCTGGCCTTGAATCAGCACATTGG
* * * * * *
588431 CACCTTTTTC-TTTCTTAAGTCCAACATCGTTGGCCTTGAATCAACATATTGG
1 CACCTTTATCATCT-TTAAGTCCAACATTGCTGGCCTTGAATCAGCACATTGG
* * ** * *
588483 CACTTTTATCATCTTTAAGACCAATGTTGCGGGCCTTGAATCAGCACATTAG
1 CACCTTTATCATCTTTAAGTCCAACATTGCTGGCCTTGAATCAGCACATTGG
* * * *
588535 CACCTTCT-TC-T-TTCTCAAGTCCAACATTGCTGGCTTTAAATCAGTATATTGG
1 CACCTT-TATCATCTT-T-AAGTCCAACATTGCTGGCCTTGAATCAGCACATTGG
* * * * * *
588587 CACCTCTATCATCTTTAAGCCCAACGTCGCTGACCTTGAATTAGCAC
1 CACCTTTATCATCTTTAAGTCCAACATTGCTGGCCTTGAATCAGCAC
588634 TTTAGCACTC
Statistics
Matches: 153, Mismatches: 42, Indels: 16
0.73 0.20 0.08
Matches are distributed among these distances:
50 2 0.01
51 5 0.03
52 139 0.91
53 5 0.03
54 2 0.01
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.35
Consensus pattern (52 bp):
CACCTTTATCATCTTTAAGTCCAACATTGCTGGCCTTGAATCAGCACATTGG
Found at i:589431 original size:20 final size:20
Alignment explanation
Indices: 589406--589456 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
589396 TACCTAGATA
*
589406 TATCGATACATTATACAGTG
1 TATCGATACATTATACAATG
*
589426 TATCGATACATTATTCAATG
1 TATCGATACATTATACAATG
589446 TATCGATACAT
1 TATCGATACAT
589457 GCAGGCTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (20 bp):
TATCGATACATTATACAATG
Found at i:594355 original size:25 final size:25
Alignment explanation
Indices: 594321--594368 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
594311 TTTTGGCATT
* *
594321 AAAACTCTTTGTTTTTCATCAAACA
1 AAAACACTTTCTTTTTCATCAAACA
594346 AAAACACTTTCTTTTTCATCAAA
1 AAAACACTTTCTTTTTCATCAAA
594369 TCTTTCTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.38, C:0.21, G:0.02, T:0.40
Consensus pattern (25 bp):
AAAACACTTTCTTTTTCATCAAACA
Found at i:603348 original size:23 final size:24
Alignment explanation
Indices: 603308--603356 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
603298 TTTTAGGGAG
603308 TTTAATCATAACTCTTAATTTAAT
1 TTTAATCATAACTCTTAATTTAAT
* * *
603332 TTTAATTA-AACTGTTAATTTTAT
1 TTTAATCATAACTCTTAATTTAAT
603355 TT
1 TT
603357 ACTTAAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.35, C:0.08, G:0.02, T:0.55
Consensus pattern (24 bp):
TTTAATCATAACTCTTAATTTAAT
Found at i:605901 original size:20 final size:20
Alignment explanation
Indices: 605876--605929 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 20
605866 GTTAGAAGCA
605876 ATGTATCGATACAATTCAT-C
1 ATGTATCGATACAATT-ATAC
605896 ATGTATCGATAC-ATTATACC
1 ATGTATCGATACAATTATA-C
605916 ATGTATCGATACAA
1 ATGTATCGATACAA
605930 ACAGTAGTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 2 0.06
19 3 0.10
20 25 0.81
21 1 0.03
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATTATAC
Found at i:610291 original size:14 final size:14
Alignment explanation
Indices: 610272--610301 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
610262 TAGCATCGAA
610272 TTAAAAAAAAACAT
1 TTAAAAAAAAACAT
*
610286 TTAAAACAAAACAT
1 TTAAAAAAAAACAT
610300 TT
1 TT
610302 GCATCCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (14 bp):
TTAAAAAAAAACAT
Found at i:614173 original size:20 final size:20
Alignment explanation
Indices: 614144--614206 Score: 71
Period size: 19 Copynumber: 3.3 Consensus size: 20
614134 TAGCTACTGC
614144 CAAT-TTCATGTATCT-ATA
1 CAATGTTCATGTATCTGATA
614162 CAATTGTTCATGTAT-TGATA
1 CAA-TGTTCATGTATCTGATA
*
614182 CAATGATCATGTATC-GATA
1 CAATGTTCATGTATCTGATA
*
614201 AAATGT
1 CAATGT
614207 ATCGATACGA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
18 3 0.08
19 20 0.53
20 15 0.39
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (20 bp):
CAATGTTCATGTATCTGATA
Found at i:621423 original size:31 final size:31
Alignment explanation
Indices: 621359--621466 Score: 117
Period size: 31 Copynumber: 3.5 Consensus size: 31
621349 GGATAAGGTG
* * * *
621359 AAACCTAATAGTCACAAAGATGATTTGAACA
1 AAACCTAATAGTCAAAAAGATGACTAGAGCA
* * * * *
621390 AAACTTATTAGTTAGAAAGATGACTAGGGCA
1 AAACCTAATAGTCAAAAAGATGACTAGAGCA
*
621421 AAACCTAATAGTCAAAAAGATGATTAGAGCA
1 AAACCTAATAGTCAAAAAGATGACTAGAGCA
*
621452 AAACCTAGTAGTCAA
1 AAACCTAATAGTCAA
621467 GAGTGAAAGC
Statistics
Matches: 62, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 62 1.00
ACGTcount: A:0.47, C:0.14, G:0.17, T:0.22
Consensus pattern (31 bp):
AAACCTAATAGTCAAAAAGATGACTAGAGCA
Found at i:622252 original size:13 final size:13
Alignment explanation
Indices: 622234--622259 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
622224 AATTTTTTTG
622234 TGTATCGATACAT
1 TGTATCGATACAT
622247 TGTATCGATACAT
1 TGTATCGATACAT
622260 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:624367 original size:21 final size:20
Alignment explanation
Indices: 624338--624380 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
624328 GACTAGTGTG
* *
624338 GGGACTGCCCGGTTGTGACCT
1 GGGACTG-CCGGTCGCGACCT
*
624359 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
624379 GG
1 GG
624381 TGGTGCTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.09, C:0.28, G:0.44, T:0.19
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:624838 original size:13 final size:13
Alignment explanation
Indices: 624820--624844 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
624810 ATAATCCCCC
624820 TGTATCGATACAG
1 TGTATCGATACAG
624833 TGTATCGATACA
1 TGTATCGATACA
624845 AAGAAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:626945 original size:15 final size:15
Alignment explanation
Indices: 626925--626955 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
626915 ATTTCGTTTG
*
626925 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
626940 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
626955 G
1 G
626956 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:628752 original size:21 final size:21
Alignment explanation
Indices: 628723--628767 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
628713 AAGTTTTTAT
*
628723 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
628743 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
628765 TTT
1 TTT
628768 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:631108 original size:20 final size:20
Alignment explanation
Indices: 631082--631138 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
631072 TACATCTTTT
631082 TCATGTATCGATACTTTGCAA
1 TCATGTATCGATACTTTG-AA
631103 -CATGTATCGATACTTTGAA
1 TCATGTATCGATACTTTGAA
**
631122 TTGTGTATCGATACTTT
1 TCATGTATCGATACTTT
631139 TAAGGGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (20 bp):
TCATGTATCGATACTTTGAA
Found at i:631536 original size:30 final size:29
Alignment explanation
Indices: 631484--631547 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 29
631474 TGACCAAAGA
* * *
631484 CAAAACCTTAGTTGAGATGGTGATTAGGG
1 CAAAACCTTAGTTGAAAAGGTGATAAGGG
* *
631513 TAAAACCTTTGGTTGAAAAGGTGATAAGGG
1 CAAAACC-TTAGTTGAAAAGGTGATAAGGG
631543 CAAAA
1 CAAAA
631548 TCTTCAATCA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
29 6 0.21
30 22 0.79
ACGTcount: A:0.38, C:0.09, G:0.28, T:0.25
Consensus pattern (29 bp):
CAAAACCTTAGTTGAAAAGGTGATAAGGG
Found at i:631688 original size:31 final size:31
Alignment explanation
Indices: 631653--631711 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
631643 GAAGGATGAC
* * * *
631653 CAAGGCGAAACCTTATAGTTACAAAGATAAT
1 CAAGGCAAAACCTAATAGATAAAAAGATAAT
631684 CAAGGCAAAACCTAATAGATAAAAAGAT
1 CAAGGCAAAACCTAATAGATAAAAAGAT
631712 GATCCTAGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.51, C:0.15, G:0.15, T:0.19
Consensus pattern (31 bp):
CAAGGCAAAACCTAATAGATAAAAAGATAAT
Found at i:631907 original size:30 final size:31
Alignment explanation
Indices: 631873--631936 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 31
631863 TTATTAGATT
* *
631873 AAAGGATGATTAGGGCAAACCT-AATCGTCA
1 AAAGGATGAATAGGGCAAACCTAAATAGTCA
*
631903 AAAGGATGAATAGGGCAAAGCTAAATAGTCA
1 AAAGGATGAATAGGGCAAACCTAAATAGTCA
631934 AAA
1 AAA
631937 AATGACCAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 20 0.67
31 10 0.33
ACGTcount: A:0.47, C:0.12, G:0.23, T:0.17
Consensus pattern (31 bp):
AAAGGATGAATAGGGCAAACCTAAATAGTCA
Found at i:632431 original size:30 final size:30
Alignment explanation
Indices: 632397--632492 Score: 83
Period size: 30 Copynumber: 3.2 Consensus size: 30
632387 AGAAACCTAA
632397 AAATGACTTAGATGAAACCAAGACTCAAAG
1 AAATGACTTAGATGAAACCAAGACTCAAAG
** * *
632427 AAATGACCTTA-ATGAAAATAGAAAC-CTAA-
1 AAATGA-CTTAGATGAAACCA-AGACTCAAAG
* *
632456 AAATGACTTGGA-CAAAGCCAAGACTCAAAG
1 AAATGACTTAGATGAAA-CCAAGACTCAAAG
632486 AAATGAC
1 AAATGAC
632493 CTTAATATAA
Statistics
Matches: 50, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
28 9 0.18
29 11 0.22
30 23 0.46
31 7 0.14
ACGTcount: A:0.51, C:0.17, G:0.16, T:0.17
Consensus pattern (30 bp):
AAATGACTTAGATGAAACCAAGACTCAAAG
Found at i:632457 original size:59 final size:58
Alignment explanation
Indices: 632386--632532 Score: 204
Period size: 59 Copynumber: 2.5 Consensus size: 58
632376 TAGATAGAAC
*
632386 TAGAAACCTAAAAATGACTTAGATGAAACCAAGACTCAAAGAAATGACCTTAATGAAAA
1 TAGAAACCTAAAAATGACTTAGATAAAACCAAGACTCAAAGAAATGACCTTAAT-AAAA
* * * *
632445 TAGAAACCTAAAAATGACTTGGACAAAGCCAAGACTCAAAGAAATGACCTTAATATAA
1 TAGAAACCTAAAAATGACTTAGATAAAACCAAGACTCAAAGAAATGACCTTAATAAAA
* * *
632503 TCAAAAACATAAAAATGACTTCGATAAAAC
1 T-AGAAACCTAAAAATGACTTAGATAAAAC
632533 TAAAACTTAA
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
58 4 0.05
59 73 0.95
ACGTcount: A:0.52, C:0.16, G:0.12, T:0.19
Consensus pattern (58 bp):
TAGAAACCTAAAAATGACTTAGATAAAACCAAGACTCAAAGAAATGACCTTAATAAAA
Found at i:632839 original size:60 final size:58
Alignment explanation
Indices: 632735--632976 Score: 213
Period size: 60 Copynumber: 4.1 Consensus size: 58
632725 GCCTAGATGG
** *
632735 AACTAGAAACCTAA-AGATGAA-TTAGGTAGAACTAAGATGCAAAGAAACAACTTGCATGA
1 AACTAGAAACCTAACA-AT-AACTTAGGTAGAACTAAGACCCAAAGAAACAACTTG-ACGA
* * * *
632794 AACTAGAAACCTAAGCAATAACTTGGGTAGAACCAAGACCCAAAGAAATAACCTAGACGA
1 AACTAGAAACCTAA-CAATAACTTAGGTAGAACTAAGACCCAAAGAAACAA-CTTGACGA
* * * ** * *
632854 AACTAGAAACCTAAAAATATCTTA-GTGGAA-TGAAGACTTAAAGAAATAGCTTAGACGA
1 AACTAGAAACCTAACAATAACTTAGGTAGAACT-AAGACCCAAAGAAACAACTT-GACGA
* * * *
632912 AATTAGAAAACTAAACAATGACTTAGGTAGAACTAAGACCCAAAGAAACAACTTGGACAA
1 AACTAGAAACCT-AACAATAACTTAGGTAGAACTAAGACCCAAAGAAACAACTT-GACGA
632972 AACTA
1 AACTA
632977 AAAGCTTAAA
Statistics
Matches: 145, Mismatches: 29, Indels: 17
0.76 0.15 0.09
Matches are distributed among these distances:
57 2 0.01
58 34 0.23
59 32 0.22
60 72 0.50
61 5 0.03
ACGTcount: A:0.50, C:0.16, G:0.17, T:0.18
Consensus pattern (58 bp):
AACTAGAAACCTAACAATAACTTAGGTAGAACTAAGACCCAAAGAAACAACTTGACGA
Found at i:633068 original size:118 final size:117
Alignment explanation
Indices: 632785--633107 Score: 315
Period size: 118 Copynumber: 2.7 Consensus size: 117
632775 AAAGAAACAA
* * * * *
632785 CTTGCATGAAACTAGAAACCTAAGCAATAACTTGGGTAGAACCAAGACCCAAAGAAATAACCTAG
1 CTTGGATGAAACTAGAAACCTAA-CAATAACTTGGGTAGAACAAAGACCCAAAGAAACAACTTGG
* ** *
632850 ACGAAACTAGAAACCTAAAAATATCTTAGTGGAATGAAGACTTAAAGAAATAG
65 ACAAAACTAGAAACCTAAAAATATCTTAGTGGAACAAAGACTTAAAAAAATAG
* * * * * * *
632903 CTTAGACGAAATTAGAAAACTAAACAATGACTTAGGTAGAACTAAGACCCAAAGAAACAACTTGG
1 CTTGGATGAAACTAGAAACCT-AACAATAACTTGGGTAGAACAAAGACCCAAAGAAACAACTTGG
* * * * *
632968 ACAAAACTA-AAAGCTTAAAAATGTCTTGGATGGAGCAAAGACTTAAAAAAATGG
65 ACAAAACTAGAAA-CCTAAAAATATCTTAG-TGGAACAAAGACTTAAAAAAATAG
* ** * * * * * *
633022 CTTGGATGAAACTAGAAACCTAATAATCTCTTGGGCAAAACAAAGACTCAAAGATACAGCTTGAA
1 CTTGGATGAAACTAGAAACCTAACAATAACTTGGGTAGAACAAAGACCCAAAGAAACAACTTGGA
**
633087 CGGAACTAGAAACCTAAAAAT
66 CAAAACTAGAAACCTAAAAAT
633108 GACATGCAAA
Statistics
Matches: 163, Mismatches: 38, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
117 3 0.02
118 119 0.73
119 41 0.25
ACGTcount: A:0.47, C:0.16, G:0.17, T:0.19
Consensus pattern (117 bp):
CTTGGATGAAACTAGAAACCTAACAATAACTTGGGTAGAACAAAGACCCAAAGAAACAACTTGGA
CAAAACTAGAAACCTAAAAATATCTTAGTGGAACAAAGACTTAAAAAAATAG
Found at i:635834 original size:21 final size:20
Alignment explanation
Indices: 635783--635839 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
635773 ATATAAACAG
*
635783 TAAATGTATCGATACATAGG
1 TAAATGTATCGATACATAGC
* *
635803 TGAATGCATCGATACAT-GCC
1 TAAATGTATCGATACATAG-C
635823 TAAAATGTATCGATACA
1 T-AAATGTATCGATACA
635840 AAACCACCTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 1 0.03
20 16 0.53
21 13 0.43
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.28
Consensus pattern (20 bp):
TAAATGTATCGATACATAGC
Found at i:643433 original size:20 final size:20
Alignment explanation
Indices: 643408--643456 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
643398 TCTGCAATAT
643408 ATCGATACATTGAATAATGC
1 ATCGATACATTGAATAATGC
** *
643428 ATCGATACATTGTGTAATGT
1 ATCGATACATTGAATAATGC
643448 ATCGATACA
1 ATCGATACA
643457 AAACTTATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (20 bp):
ATCGATACATTGAATAATGC
Found at i:649462 original size:13 final size:13
Alignment explanation
Indices: 649444--649469 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
649434 CATATCCAGA
649444 TGTATCGATACAT
1 TGTATCGATACAT
649457 TGTATCGATACAT
1 TGTATCGATACAT
649470 GTTCATTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:649478 original size:19 final size:19
Alignment explanation
Indices: 649454--649509 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
649444 TGTATCGATA
*
649454 CATTGTATCGATACATGTT
1 CATTGTATCGATACATGCT
* *
649473 CATTGTATCAATACATACT
1 CATTGTATCGATACATGCT
*
649492 CAATTGTATTGATACATG
1 C-ATTGTATCGATACATG
649510 AGAGTGGCAG
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.39
Consensus pattern (19 bp):
CATTGTATCGATACATGCT
Found at i:649981 original size:14 final size:15
Alignment explanation
Indices: 649957--649986 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
649947 TTATTTAGAG
649957 GCAATTTTCGTTTGT
1 GCAATTTTCGTTTGT
649972 GCAA-TTTCGTTTGT
1 GCAATTTTCGTTTGT
649986 G
1 G
649987 TAAGGTTGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.13, C:0.13, G:0.23, T:0.50
Consensus pattern (15 bp):
GCAATTTTCGTTTGT
Found at i:650039 original size:23 final size:23
Alignment explanation
Indices: 650004--650048 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
649994 GCATTCAACC
*
650004 TTGGGTTACAATTTCTTA-AGAAT
1 TTGGGGTACAA-TTCTTAGAGAAT
*
650027 TTGGGGTATAATTCTTAGAGAA
1 TTGGGGTACAATTCTTAGAGAA
650049 ATTATGAGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.31, C:0.07, G:0.22, T:0.40
Consensus pattern (23 bp):
TTGGGGTACAATTCTTAGAGAAT
Found at i:650987 original size:2 final size:2
Alignment explanation
Indices: 650982--651010 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
650972 TTTTTAAAAG
650982 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
651011 ATGTTTCTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:656187 original size:12 final size:12
Alignment explanation
Indices: 656170--656196 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
656160 ACTTGTTTGG
656170 TGCTTGTTTCCA
1 TGCTTGTTTCCA
656182 TGCTTGTTTCCA
1 TGCTTGTTTCCA
656194 TGC
1 TGC
656197 ATTTCCATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.26, G:0.19, T:0.48
Consensus pattern (12 bp):
TGCTTGTTTCCA
Found at i:656325 original size:33 final size:33
Alignment explanation
Indices: 656282--656346 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
656272 TTTGGGACAA
656282 TGTATCGATACAAT-T-CTTCATGTATCGATACAT
1 TGTATCGATACAATGTGC--CATGTATCGATACAT
*
656315 TGTATTGATACAATGTGCCATGTATCGATACA
1 TGTATCGATACAATGTGCCATGTATCGATACA
656347 AAAAGTGGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (33 bp):
TGTATCGATACAATGTGCCATGTATCGATACAT
Found at i:656421 original size:19 final size:20
Alignment explanation
Indices: 656397--656448 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
656387 ACAATTATGT
*
656397 ATGTATCGATACAATG-A-A
1 ATGTATCGATACAAAGCATA
656415 CATGTATCGATACAAAGCATA
1 -ATGTATCGATACAAAGCATA
656436 ATGTATCGATACA
1 ATGTATCGATACA
656449 TCTAGATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 15 0.50
20 14 0.47
21 1 0.03
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (20 bp):
ATGTATCGATACAAAGCATA
Found at i:662482 original size:13 final size:13
Alignment explanation
Indices: 662464--662500 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
662454 GTAACCCATG
*
662464 TATCGATACATTA
1 TATCGATACAATA
*
662477 TATCGATACAATG
1 TATCGATACAATA
662490 TATCGATACAA
1 TATCGATACAA
662501 AGAACATTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (13 bp):
TATCGATACAATA
Found at i:667071 original size:15 final size:15
Alignment explanation
Indices: 667053--667087 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
667043 CGAGTCAACT
667053 TCATCATTATCATCA
1 TCATCATTATCATCA
*
667068 TCATCATTATCTTCA
1 TCATCATTATCATCA
667083 TCATC
1 TCATC
667088 TTTGATGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (15 bp):
TCATCATTATCATCA
Found at i:670691 original size:13 final size:13
Alignment explanation
Indices: 670673--670708 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
670663 ATTTATGATG
*
670673 TATCGATACACTA
1 TATCGATACAATA
*
670686 TATCGATACAATG
1 TATCGATACAATA
670699 TATCGATACA
1 TATCGATACA
670709 TGAATAATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (13 bp):
TATCGATACAATA
Found at i:670820 original size:22 final size:22
Alignment explanation
Indices: 670766--670820 Score: 103
Period size: 21 Copynumber: 2.5 Consensus size: 22
670756 GTGAACAGTG
670766 TGAACAGTGATGTATCGATACA
1 TGAACAGTGATGTATCGATACA
670788 TGAA-AGTGATGTATCGATACA
1 TGAACAGTGATGTATCGATACA
670809 TGAACAGTGATG
1 TGAACAGTGATG
670821 AATAGTGATG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.66
22 11 0.34
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.27
Consensus pattern (22 bp):
TGAACAGTGATGTATCGATACA
Found at i:670827 original size:10 final size:10
Alignment explanation
Indices: 670808--670838 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
670798 GTATCGATAC
670808 ATGAACAGTG
1 ATGAACAGTG
*
670818 ATGAATAGTG
1 ATGAACAGTG
670828 ATGAACAGTG
1 ATGAACAGTG
670838 A
1 A
670839 CAATGAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:670926 original size:53 final size:53
Alignment explanation
Indices: 670862--670998 Score: 220
Period size: 53 Copynumber: 2.6 Consensus size: 53
670852 CTACTACCAA
* *
670862 TGTATCGATACATATTTTGTATATCGATACAAATTTGGCTACTGCCAGTGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* *
670915 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
*
670968 TGTATCGATACATATTTGTGTGTATCAATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
670999 TATGCAATCT
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
53 65 0.84
54 12 0.16
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.37
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:671104 original size:21 final size:21
Alignment explanation
Indices: 671078--671118 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
671068 GTCAACCTTG
671078 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
671099 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
671119 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:672458 original size:32 final size:32
Alignment explanation
Indices: 672320--672486 Score: 154
Period size: 33 Copynumber: 5.4 Consensus size: 32
672310 TCCTCCAAAC
672320 TTTTC-TCAAAAGTCCACAACTCCATGGCACC-
1 TTTTCTTC-AAAGTCCACAACTCCATGGCACCT
*
672351 -TTT-TT--AAGTCCACAACTCTATGGCA--T
1 TTTTCTTCAAAGTCCACAACTCCATGGCACCT
* * *** *
672377 TTTT-TTTAAAGTCCACAGCTTTGTGGTACCT
1 TTTTCTTCAAAGTCCACAACTCCATGGCACCT
*
672408 TTTTCTTCTAAAGTCCACAACTCCGTGGCACCT
1 TTTTCTTC-AAAGTCCACAACTCCATGGCACCT
*
672441 TTTTCTTCAAAGTCCACAACTTCATGGCACCT
1 TTTTCTTCAAAGTCCACAACTCCATGGCACCT
672473 TTTAGTCTTCAAAG
1 TTT--TCTTCAAAG
672487 AGAAGGATGC
Statistics
Matches: 113, Mismatches: 12, Indels: 19
0.78 0.08 0.13
Matches are distributed among these distances:
27 24 0.21
29 16 0.14
30 4 0.04
31 5 0.04
32 27 0.24
33 28 0.25
34 9 0.08
ACGTcount: A:0.25, C:0.28, G:0.12, T:0.36
Consensus pattern (32 bp):
TTTTCTTCAAAGTCCACAACTCCATGGCACCT
Found at i:672625 original size:39 final size:39
Alignment explanation
Indices: 672542--672630 Score: 117
Period size: 39 Copynumber: 2.3 Consensus size: 39
672532 CTTTTTAGTT
* * *
672542 CTCAAAGGGCAAGATGCATTTTCTTCTTTTCCTTTCATC
1 CTCAAAGAGCAAGATGCACTTTATTCTTTTCCTTTCATC
* *
672581 TTCAAAGAGCAAGATGCACTTTATTCTTTTCCCTTT-GTC
1 CTCAAAGAGCAAGATGCACTTTATTCTTTT-CCTTTCATC
672620 CTCAAAGAGCA
1 CTCAAAGAGCA
672631 TGACACACTT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 38 0.88
40 5 0.12
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.37
Consensus pattern (39 bp):
CTCAAAGAGCAAGATGCACTTTATTCTTTTCCTTTCATC
Found at i:672640 original size:39 final size:39
Alignment explanation
Indices: 672542--672640 Score: 92
Period size: 39 Copynumber: 2.5 Consensus size: 39
672532 CTTTTTAGTT
* ** * *
672542 CTCAAAGGGCAAGATGCATTTTCTTCTTTTCCTTTCATC
1 CTCAAAGAGCAAGACACACTTTATTCTTTTCCTTTCATC
* ** *
672581 TTCAAAGAGCAAGATGCACTTTATTCTTTTCCCTTT-GTC
1 CTCAAAGAGCAAGACACACTTTATTCTTTT-CCTTTCATC
*
672620 CTCAAAGAGCATGACACACTT
1 CTCAAAGAGCAAGACACACTT
672641 CATTTCCTTT
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
39 45 0.90
40 5 0.10
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.36
Consensus pattern (39 bp):
CTCAAAGAGCAAGACACACTTTATTCTTTTCCTTTCATC
Found at i:672728 original size:81 final size:80
Alignment explanation
Indices: 672568--672757 Score: 184
Period size: 81 Copynumber: 2.3 Consensus size: 80
672558 CATTTTCTTC
* * * *
672568 TTTTCCTTTCATCTTCAAAGAGCAAGATGCACTTTA-TTCTTTTCCCTTTGTCCTCAAAGAGCAT
1 TTTTCCTTT-ATCTTCAAAGAGCAGGATGC-C--CACTCCTTTTCCCTTTGTCCTCAAAGAGCAA
**
672632 GACACACTTCATTTCCTTT
62 GACACACTTCATTTCCCCT
* * * * * *
672651 TCTTTCTTTTGTCTTTAAAGAGCAGGATGCCCACTCCTTTTCCCTTTGTCCTGAAGGAGTAAGAC
1 T-TTTCCTTTATCTTCAAAGAGCAGGATGCCCACTCCTTTTCCCTTTGTCCTCAAAGAGCAAGAC
* ** *
672716 CCTTTTCTTTTCCCCT
65 ACACTTCATTTCCCCT
672732 TTTTCCTTTATCTTCAAAGAGCAGGA
1 TTTTCCTTTATCTTCAAAGAGCAGGA
672758 CCTATTTCAT
Statistics
Matches: 86, Mismatches: 19, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
80 23 0.27
81 37 0.43
82 1 0.01
83 18 0.21
84 7 0.08
ACGTcount: A:0.21, C:0.26, G:0.13, T:0.41
Consensus pattern (80 bp):
TTTTCCTTTATCTTCAAAGAGCAGGATGCCCACTCCTTTTCCCTTTGTCCTCAAAGAGCAAGACA
CACTTCATTTCCCCT
Found at i:672895 original size:31 final size:32
Alignment explanation
Indices: 672860--672945 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 32
672850 TTCTCTTTCT
672860 AAAGCCCACACGAGTTGCTGGCATCC-AAGTC
1 AAAGCCCACACGAGTTGCTGGCATCCTAAGTC
*** * *
672891 AAAGCTTGCACAAGTTGGC-GGCA-CCTGAGTC
1 AAAGCCCACACGAGTT-GCTGGCATCCTAAGTC
*
672922 AAAGCCCACACGAGTTGGTGGCAT
1 AAAGCCCACACGAGTTGCTGGCAT
672946 TTAAGTTCAA
Statistics
Matches: 41, Mismatches: 10, Indels: 7
0.71 0.17 0.12
Matches are distributed among these distances:
30 3 0.07
31 36 0.88
32 2 0.05
ACGTcount: A:0.28, C:0.28, G:0.27, T:0.17
Consensus pattern (32 bp):
AAAGCCCACACGAGTTGCTGGCATCCTAAGTC
Found at i:673041 original size:31 final size:31
Alignment explanation
Indices: 673003--673089 Score: 93
Period size: 31 Copynumber: 2.8 Consensus size: 31
672993 CTTAAAATGC
* *
673003 CAAAGCCTACATGAGTTGGTGGCACCCTAGT
1 CAAAGCCTGCATGAGTTGGTGGCACCCAAGT
* *** *
673034 CAAAGCCTGCATAAGTTGCCAGCACCGAAGT
1 CAAAGCCTGCATGAGTTGGTGGCACCCAAGT
* *
673065 CAAAGCCCGCACGAGTTGGTGGCAC
1 CAAAGCCTGCATGAGTTGGTGGCAC
673090 TTAAGTTCGA
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.28, C:0.29, G:0.26, T:0.17
Consensus pattern (31 bp):
CAAAGCCTGCATGAGTTGGTGGCACCCAAGT
Found at i:673170 original size:149 final size:148
Alignment explanation
Indices: 672860--673600 Score: 893
Period size: 149 Copynumber: 5.0 Consensus size: 148
672850 TTCTCTTTCT
* * * *
672860 AAAGCCCACACGAGTTGCTGGCATCCAAGTCAAAGCTTGCACAAGTTGGCGGCACCTGAGTCAAA
1 AAAGCCCACACGAGTTGGTGGCACCCTAGTCAAAGCCTGCACAAGTTGGCGGCACC-GAGTCAAA
* * * *
672925 GCCCACACGAGTTGGTGGCATTTAAG-T----TCAAGTCTATATTAGTTGGCACTTGTCTAAGGA
65 GCCCACACGAGTTGGTGGCACTTAAGTTCGAGTCAAGTCCACATTAGTTGGCACCTGTCTAAGGA
* *
672985 GGTTAAGCCTTAAAATGCC
130 GGTTAAGCCTTAGAATGTC
* * * * *
673004 AAAGCCTACATGAGTTGGTGGCACCCTAGTCAAAGCCTGCATAAGTTGCCAGCACCGAAGTCAAA
1 AAAGCCCACACGAGTTGGTGGCACCCTAGTCAAAGCCTGCACAAGTTGGCGGCACCG-AGTCAAA
*
673069 GCCCGCACGAGTTGGTGGCACTTAAGTTCGAGTCAAGTCCACATTAGTTGGCACCTGTCTAAGGA
65 GCCCACACGAGTTGGTGGCACTTAAGTTCGAGTCAAGTCCACATTAGTTGGCACCTGTCTAAGGA
673134 GGTTAAGCCTTAGAATGTC
130 GGTTAAGCCTTAGAATGTC
* * *
673153 AAAGCCCACACAAGTTGGTGGCACCCTAGTCAAAGCCTGCATAAGTTGGTGGCATCCGAGTCAAA
1 AAAGCCCACACGAGTTGGTGGCACCCTAGTCAAAGCCTGCACAAGTTGGCGGCA-CCGAGTCAAA
* * * *
673218 GCTCACACGAGTTGGTGGCACTTAAGTTCGAGTCAAGTCTACAATAGTTGGCACTTGTCTAAGGA
65 GCCCACACGAGTTGGTGGCACTTAAGTTCGAGTCAAGTCCACATTAGTTGGCACCTGTCTAAGGA
673283 GGTTAAGCCTTAGAATGTC
130 GGTTAAGCCTTAGAATGTC
* ** * *
673302 AAAGCCCACATGAGTTGGTGGCACCCTAGTCAAAGCCCACACAAGTTGGCAGCACCCTAGTCAAA
1 AAAGCCCACACGAGTTGGTGGCACCCTAGTCAAAGCCTGCACAAGTTGGCGGCA-CCGAGTCAAA
* ** * * *
673367 GGCCACATAAGTTGGTGGCACCTAAGTTTGAGTCAAGTCCACATTGGTTGGCACCTGTCTAAGGA
65 GCCCACACGAGTTGGTGGCACTTAAGTTCGAGTCAAGTCCACATTAGTTGGCACCTGTCTAAGGA
** * *
673432 GGTTAAGCGAATGGCACCCAAGTC
130 GGTTAAGC-CTTAG-A---ATGTC
* * *
673456 AAAGCCCACACGAGTTGGTGACACCCTAGTCAAAGCCTGCGCAAGTTGGCGGCACTCGAGTCAAT
1 AAAGCCCACACGAGTTGGTGGCACCCTAGTCAAAGCCTGCACAAGTTGGCGGCAC-CGAGTCAAA
** * * * * *
673521 GCCTGCACAAGTTGGTGGCACCTAAG-TCTGAGTCAAGTCCACTTTAGTTGCCACCTAG-CTGAG
65 GCCCACACGAGTTGGTGGCACTTAAGTTC-GAGTCAAGTCCACATTAGTTGGCACCT-GTCTAAG
673584 GAGGTTAAGCCTTAGAA
128 GAGGTTAAGCCTTAGAA
673601 AACCAAAACT
Statistics
Matches: 512, Mismatches: 70, Indels: 25
0.84 0.12 0.04
Matches are distributed among these distances:
143 1 0.00
144 78 0.15
145 1 0.00
149 301 0.59
150 5 0.01
151 1 0.00
152 1 0.00
153 4 0.01
154 119 0.23
155 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.25, T:0.23
Consensus pattern (148 bp):
AAAGCCCACACGAGTTGGTGGCACCCTAGTCAAAGCCTGCACAAGTTGGCGGCACCGAGTCAAAG
CCCACACGAGTTGGTGGCACTTAAGTTCGAGTCAAGTCCACATTAGTTGGCACCTGTCTAAGGAG
GTTAAGCCTTAGAATGTC
Found at i:673188 original size:31 final size:31
Alignment explanation
Indices: 673150--673238 Score: 115
Period size: 31 Copynumber: 2.9 Consensus size: 31
673140 GCCTTAGAAT
*
673150 GTCAAAGCCCACACAAGTTGGTGGCACCCTA
1 GTCAAAGCCCACACAAGTTGGTGGCACCCGA
** * *
673181 GTCAAAGCCTGCATAAGTTGGTGGCATCCGA
1 GTCAAAGCCCACACAAGTTGGTGGCACCCGA
* *
673212 GTCAAAGCTCACACGAGTTGGTGGCAC
1 GTCAAAGCCCACACAAGTTGGTGGCAC
673239 TTAAGTTCGA
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (31 bp):
GTCAAAGCCCACACAAGTTGGTGGCACCCGA
Found at i:673337 original size:31 final size:31
Alignment explanation
Indices: 673299--673388 Score: 135
Period size: 31 Copynumber: 2.9 Consensus size: 31
673289 GCCTTAGAAT
*
673299 GTCAAAGCCCACATGAGTTGGTGGCACCCTA
1 GTCAAAGCCCACATAAGTTGGTGGCACCCTA
* **
673330 GTCAAAGCCCACACAAGTTGGCAGCACCCTA
1 GTCAAAGCCCACATAAGTTGGTGGCACCCTA
*
673361 GTCAAAGGCCACATAAGTTGGTGGCACC
1 GTCAAAGCCCACATAAGTTGGTGGCACC
673389 TAAGTTTGAG
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.29, C:0.30, G:0.24, T:0.17
Consensus pattern (31 bp):
GTCAAAGCCCACATAAGTTGGTGGCACCCTA
Found at i:673503 original size:31 final size:31
Alignment explanation
Indices: 673443--673542 Score: 110
Period size: 31 Copynumber: 3.2 Consensus size: 31
673433 GTTAAGCGAA
* ** *
673443 TGGCACCCAAGTCAAAGCCCACACGAGTTGG
1 TGGCACCCGAGTCAAAGCCTGCACAAGTTGG
* * *
673474 TGACACCCTAGTCAAAGCCTGCGCAAGTTGG
1 TGGCACCCGAGTCAAAGCCTGCACAAGTTGG
* * *
673505 CGGCACTCGAGTCAATGCCTGCACAAGTTGG
1 TGGCACCCGAGTCAAAGCCTGCACAAGTTGG
673536 TGGCACC
1 TGGCACC
673543 TAAGTCTGAG
Statistics
Matches: 55, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 55 1.00
ACGTcount: A:0.25, C:0.31, G:0.27, T:0.17
Consensus pattern (31 bp):
TGGCACCCGAGTCAAAGCCTGCACAAGTTGG
Found at i:674092 original size:21 final size:20
Alignment explanation
Indices: 674068--674144 Score: 73
Period size: 21 Copynumber: 3.8 Consensus size: 20
674058 TTCTAAAATT
674068 TGTATCGATACAAATAGTAAA
1 TGTATCGATACAAA-AGTAAA
* *
674089 TGTATCGATACATAAGTGAA
1 TGTATCGATACAAAAGTAAA
* ****
674109 TGTATTGATACATGCCTAAAA
1 TGTATCGATACAAAAGT-AAA
674130 TGTATCGATACAAAA
1 TGTATCGATACAAAA
674145 CCACCCTGCA
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 18 0.41
21 26 0.59
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.30
Consensus pattern (20 bp):
TGTATCGATACAAAAGTAAA
Found at i:674112 original size:20 final size:21
Alignment explanation
Indices: 674068--674121 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
674058 TTCTAAAATT
*
674068 TGTATCGATACAAATAGTAAA
1 TGTATCGATACATATAGTAAA
*
674089 TGTATCGATACATA-AGTGAA
1 TGTATCGATACATATAGTAAA
*
674109 TGTATTGATACAT
1 TGTATCGATACAT
674122 GCCTAAAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.33
Consensus pattern (21 bp):
TGTATCGATACATATAGTAAA
Found at i:677863 original size:81 final size:80
Alignment explanation
Indices: 677673--677898 Score: 211
Period size: 81 Copynumber: 2.8 Consensus size: 80
677663 TGGAAAACTT
* * * *
677673 GATGTTTTTGGAAATACAGACGAGGTTGGAGTATCCCTTCAAAAATGGTGGGGTTGGAGTATCCT
1 GATGTTTTTGGAAACA-AAACGAGGTTGGAGTATCCCTTCAAAAATGGTGGAGTTGAAGTATCCT
* ** *
677738 CGAAGATGGAAAGTTT
65 CGAAGATGAAAAAATC
* * ** * *
677754 GTTGTTTTTTGAAACAAAAATATAGTTGGAGTATCGCC-TCGAAAATGGTGGAGTTGAAGTATCC
1 GATGTTTTTGGAAACAAAACGA-GGTTGGAGTATC-CCTTCAAAAATGGTGGAGTTGAAGTATCC
677818 TCGAAGATGAAAAAATC
64 TCGAAGATGAAAAAATC
* ** ** * * *
677835 GATGTTTTTGGAAGCAACGGCGAGGTTGGAGTATCTTTTCAAAAATAGTGGGGTTGGAGTATCC
1 GATGTTTTTGGAAACAA-AACGAGGTTGGAGTATCCCTTCAAAAATGGTGGAGTTGAAGTATCC
677899 CCATTTAATG
Statistics
Matches: 113, Mismatches: 28, Indels: 8
0.76 0.19 0.05
Matches are distributed among these distances:
80 3 0.03
81 107 0.95
82 3 0.03
ACGTcount: A:0.30, C:0.11, G:0.29, T:0.30
Consensus pattern (80 bp):
GATGTTTTTGGAAACAAAACGAGGTTGGAGTATCCCTTCAAAAATGGTGGAGTTGAAGTATCCTC
GAAGATGAAAAAATC
Found at i:683349 original size:13 final size:13
Alignment explanation
Indices: 683331--683359 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
683321 CTTCCTAGCC
683331 AAAAAAAACAAAA
1 AAAAAAAACAAAA
683344 AAAAAAAACAAAA
1 AAAAAAAACAAAA
683357 AAA
1 AAA
683360 CCAAGGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAACAAAA
Found at i:683382 original size:22 final size:22
Alignment explanation
Indices: 683330--683382 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
683320 CCTTCCTAGC
*
683330 CAAAAAAAACAAAAAAAAAAAA
1 CAAAAAAACCAAAAAAAAAAAA
** *
683352 CAAAAAAACCAAGGAAAAATAA
1 CAAAAAAACCAAAAAAAAAAAA
683374 CAAAAAAAC
1 CAAAAAAAC
683383 AGAAAGGGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.81, C:0.13, G:0.04, T:0.02
Consensus pattern (22 bp):
CAAAAAAACCAAAAAAAAAAAA
Found at i:684638 original size:28 final size:28
Alignment explanation
Indices: 684598--685166 Score: 520
Period size: 28 Copynumber: 19.9 Consensus size: 28
684588 CGTTCATCTC
* *
684598 TTCAACGCCCACAAGTCAGCGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
684626 TTCAAAGCCCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
684655 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
684683 TCCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
** * *
684711 TTCAAAGCCCAGGAGTCGGTGGCGACTCTT
1 TTCAAAGCCCACAAGTCAGTGGC-AC-CCT
*
684741 TTCAAAGCCCATAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* ** * *
684769 TTCAAAGCCCACGAGTTGGTGGTAACTCTT
1 TTCAAAGCCCACAAGTCAGTGG-CAC-CCT
* *
684799 TTCAAAGCGCACAAG---GTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
684824 TTCAAAGCCCACAAGTCAGTGGCATCCG
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
684852 TTCAAAGCCCACGAGTCGGTGGCAACTCTT
1 TTCAAAGCCCACAAGTCAGTGGC-AC-CCT
* *
684882 TTCAAAGCCCACAAGTCAGTGGCATTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-CCCT
* * *
684911 TTCAAAGCCCATAAGTCAATGGCACCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
684939 TTCAAA--CCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
** * * *
684965 TTTGAAGCCCATAAGTCAGTGGTATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
** *
684993 TTCAAAGCATACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * * *
685021 TTCAAAGCCCACGAGTCGGT-ACAACTCT
1 TTCAAAGCCCACAAGTCAGTGGC-ACCCT
685049 TCTCAAAGCCCACAAGTCAGTGGCACCCT
1 T-TCAAAGCCCACAAGTCAGTGGCACCCT
* * *
685078 TTCAAAGCCCACTAGTCGGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
** *
685107 TTCAAAGCCCACACGAGTCAGTGATAACTCTT
1 TTCAAAGCCCACA--AGTCAGTG-GCAC-CCT
*
685139 TTCAAAGCCTACACAAGTTAGTGGCACC
1 TTCAAAGCC--CACAAGTCAGTGGCACC
685167 TTTTTTTAGA
Statistics
Matches: 444, Mismatches: 75, Indels: 42
0.79 0.13 0.07
Matches are distributed among these distances:
25 16 0.04
26 21 0.05
27 5 0.01
28 211 0.48
29 95 0.21
30 61 0.14
31 9 0.02
32 22 0.05
34 4 0.01
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.23
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCT
Found at i:684856 original size:141 final size:140
Alignment explanation
Indices: 684598--685129 Score: 574
Period size: 141 Copynumber: 3.7 Consensus size: 140
684588 CGTTCATCTC
* *
684598 TTCAACGCCCACAAGTCAGCGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAG-
* * *
684663 CCACAAGTCAGTGGCACCCTTCCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCAGGAGTC
65 CCACAAG--AGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACGAGTC
*
684728 GGTGGCGACTCTT
128 GGTGGCAACTCTT
* * ** *
684741 TTCAAAGCCCATAAGTCAGTGGCACCCTTTCAAAGCCCACGAGTTGGTGGTAACTCTTTTCAAAG
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGG-CACTCTTTTCAAAG
*
684806 CGCACAAG-GTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCGTTCAAAGCCCACGAGTCG
65 C-CACAAGAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACGAGTCG
684870 GTGGCAACTCTT
129 GTGGCAACTCTT
* * * *
684882 TTCAAAGCCCACAAGTCAGTGGCATTCTTTTCAAAGCCCATAAGTCAATGGCAC-CTTTTCAAA-
1 TTCAAAGCCCACAAGTCAGTGGCA-CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAG
** * * ** *
684945 CCACAAGTCAGTGGCATCCTTTTGAAGCCCATAAGTCAGTGGTATCCTTTCAAAGCATACAAGTC
65 CCACAAG--AGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACGAGTC
* *
685010 AGTGGC-A-TCCT
128 GGTGGCAACTCTT
* * * * *
685021 TTCAAAGCCCACGAGTCGGT-ACAACTCTTCTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAA
1 TTCAAAGCCCACAAGTCAGTGGC-ACCCTT-TCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
* * *
685084 GCCCACTAGTCGGTGGCACTCTTTTCAAAGCCCACACGAGTCAGTG
64 G-CCACAAG--AGTGGCA-TCCTTTCAAAGCCCACA--AGTCAGTG
685130 ATAACTCTTT
Statistics
Matches: 330, Mismatches: 46, Indels: 25
0.82 0.11 0.06
Matches are distributed among these distances:
138 9 0.03
139 53 0.16
140 10 0.03
141 154 0.47
142 32 0.10
143 45 0.14
144 27 0.08
ACGTcount: A:0.27, C:0.31, G:0.20, T:0.23
Consensus pattern (140 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGC
CACAAGAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACGAGTCGGT
GGCAACTCTT
Found at i:684949 original size:113 final size:112
Alignment explanation
Indices: 684606--685170 Score: 547
Period size: 113 Copynumber: 5.0 Consensus size: 112
684596 TCTTCAACGC
* *
684606 CCACAAGTCAGCGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGT
1 CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGT
* * *
684671 CAGTGGCACCCTTCCAAAGCCCACAAGTCAGTGGCATCC-TTTCAAAG
66 CAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAG
* * * *
684718 CC-CAGGAGTCGGTGGCGACTCTTTTCAAAGCCCATAAGTCAGTGGCAC-CCTTTCAAAGCCCAC
1 CCACA--AGTCAGTGGC-A-TCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCAC
* ** * *
684781 GAGTTGGTGGTAACTCTTTTCAAAGCGCACAAG---GTGGCATCC-TTTCAAAG
62 AAGTCAGTGG-CA-TCTTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAG
* * *
684831 CCCACAAGTCAGTGGCATCCGTTCAAAGCCCACGAGTCGGTGGCAACTCTTTTCAAAGCCCACAA
1 -CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGC-ACTCTTTTCAAAGCCCACAA
* *
684896 GTCAGTGGCATTCTTTTCAAAGCCCATAAGTCAATGGCACCTTTTCAAA-
64 GTCAGTGGCA-TCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAG
** * * * **
684945 CCACAAGTCAGTGGCATCCTTTTGAAGCCCATAAGTCAGTGGTA-TCCTTTCAAAGCATACAAGT
1 CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGT
* * * * *
685009 CAGTGGCATCCTTTCAAAGCCCACGAGTCGGT-ACAACTCTTCTCAAAG
66 CAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGC-AC-CTTTTCAAAG
* * *
685057 CCCACAAGTCAGTGGCACCCTTTCAAAGCCCACTAGTCGGTGGCACTCTTTTCAAAGCCCACACG
1 -CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACA--
** *
685122 AGTCAGTGATAACTCTTTTCAAAGCCTACACAAGTTAGTGGCACCTTTT
63 AGTCAGTG-GCA-TCTTTTCAAAGCC--CACAAGTCAGTGGCACCTTTT
685171 TTTAGAAAAA
Statistics
Matches: 363, Mismatches: 64, Indels: 45
0.77 0.14 0.10
Matches are distributed among these distances:
109 1 0.00
110 21 0.06
111 57 0.16
112 24 0.07
113 128 0.35
114 40 0.11
115 41 0.11
116 23 0.06
117 1 0.00
118 12 0.03
119 4 0.01
120 10 0.03
121 1 0.00
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.23
Consensus pattern (112 bp):
CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGT
CAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAG
Found at i:686108 original size:40 final size:40
Alignment explanation
Indices: 686048--686139 Score: 130
Period size: 40 Copynumber: 2.3 Consensus size: 40
686038 TGCCCAGATA
686048 TATCGATACATTTTGCAATGTATCAAAACATGTATGAAAG
1 TATCGATACATTTTGCAATGTATCAAAACATGTATGAAAG
* ** * * *
686088 TATCAATACATTTTTTAATGTATCGATACATGTATGAACG
1 TATCGATACATTTTGCAATGTATCAAAACATGTATGAAAG
686128 TATCGATACATT
1 TATCGATACATT
686140 CTGTCTTTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (40 bp):
TATCGATACATTTTGCAATGTATCAAAACATGTATGAAAG
Found at i:686116 original size:20 final size:20
Alignment explanation
Indices: 686048--686139 Score: 87
Period size: 20 Copynumber: 4.6 Consensus size: 20
686038 TGCCCAGATA
686048 TATCGATACATTT-TGCAATG
1 TATCGATACATTTATG-AATG
* * * *
686068 TATCAAAACATGTATGAAAG
1 TATCGATACATTTATGAATG
* * *
686088 TATCAATACATTTTTTAATG
1 TATCGATACATTTATGAATG
* *
686108 TATCGATACATGTATGAACG
1 TATCGATACATTTATGAATG
686128 TATCGATACATT
1 TATCGATACATT
686140 CTGTCTTTTT
Statistics
Matches: 56, Mismatches: 15, Indels: 2
0.77 0.21 0.03
Matches are distributed among these distances:
20 54 0.96
21 2 0.04
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (20 bp):
TATCGATACATTTATGAATG
Found at i:688680 original size:25 final size:24
Alignment explanation
Indices: 688641--688688 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
688631 TCATCCACAG
688641 GGATATCCAACCCCATCTTCTAAAA
1 GGATATCCAACCCCA-CTTCTAAAA
*
688666 GGATACTCCAA-CCCACTTTTAAA
1 GGATA-TCCAACCCCACTTCTAAA
688689 CTCGTTAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 7 0.33
25 9 0.43
26 5 0.24
ACGTcount: A:0.35, C:0.31, G:0.08, T:0.25
Consensus pattern (24 bp):
GGATATCCAACCCCACTTCTAAAA
Found at i:692750 original size:12 final size:12
Alignment explanation
Indices: 692733--692757 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
692723 TTGAAGATCG
692733 TAATTTATTTAT
1 TAATTTATTTAT
692745 TAATTTATTTAT
1 TAATTTATTTAT
692757 T
1 T
692758 TTCTAAAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TAATTTATTTAT
Found at i:702864 original size:43 final size:43
Alignment explanation
Indices: 702799--702900 Score: 186
Period size: 43 Copynumber: 2.4 Consensus size: 43
702789 ATACAATGTC
* *
702799 TCATGTATCAATACAAATAGTGATAGGATAGCTACTGCTAGTT
1 TCATGTATCGATACAAACAGTGATAGGATAGCTACTGCTAGTT
702842 TCATGTATCGATACAAACAGTGATAGGATAGCTACTGCTAGTT
1 TCATGTATCGATACAAACAGTGATAGGATAGCTACTGCTAGTT
702885 TCATGTATCGATACAA
1 TCATGTATCGATACAA
702901 TTCTTCATGT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (43 bp):
TCATGTATCGATACAAACAGTGATAGGATAGCTACTGCTAGTT
Found at i:702909 original size:20 final size:20
Alignment explanation
Indices: 702884--702940 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 20
702874 TACTGCTAGT
*
702884 TTCATGTATCGATACAATTC
1 TTCATGTATTGATACAATTC
*
702904 TTCATGTATTGATACAA-TG
1 TTCATGTATTGATACAATTC
*
702923 ATCATGTATTGATACAAT
1 TTCATGTATTGATACAAT
702941 GTATTGATAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.40
Consensus pattern (20 bp):
TTCATGTATTGATACAATTC
Found at i:702944 original size:13 final size:13
Alignment explanation
Indices: 702926--702952 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
702916 TACAATGATC
702926 ATGTATTGATACA
1 ATGTATTGATACA
702939 ATGTATTGATACA
1 ATGTATTGATACA
702952 A
1 A
702953 AGCAATATGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (13 bp):
ATGTATTGATACA
Found at i:704354 original size:13 final size:13
Alignment explanation
Indices: 704336--704361 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
704326 CAATTTTTTG
704336 TGTATCGATACAT
1 TGTATCGATACAT
704349 TGTATCGATACAT
1 TGTATCGATACAT
704362 ACTTGCTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:706925 original size:13 final size:13
Alignment explanation
Indices: 706907--706945 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
706897 ATAATCACCC
*
706907 TGTATCGATACAG
1 TGTATCGATACAA
706920 TGTATCGATACAA
1 TGTATCGATACAA
706933 TGTATCGATACAA
1 TGTATCGATACAA
706946 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:706956 original size:20 final size:20
Alignment explanation
Indices: 706931--707009 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
706921 GTATCGATAC
706931 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
706951 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
706976 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
706996 CATGTATCGATACA
1 AATGTATCGATACA
707010 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:709040 original size:15 final size:15
Alignment explanation
Indices: 709020--709050 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
709010 ATTTCGTTTG
*
709020 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
709035 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
709050 G
1 G
709051 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Done.